> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/illumina-trupath-genome/additional-information/known-limitations.md).

# Known Limitations

#### Functionality <a href="#functionality" id="functionality"></a>

* This software solution will only work with the Illumina TruPath Genome prep on the Nova Seq X Instrument Series
  * NovaSeq X Instrument must be upgraded to 1.4 SW.
  * Indexing is currently not supported with the Illumina TruPath Genome prep. One sample per flow cell lane is currently supported.
  * Using non-TruPath data inputs to DRAGEN will lead to analysis failure.

#### Performance <a href="#performance" id="performance"></a>

* Due to FPGA memory limitations, on-prem analysis for the Illumina TruPath Genome requires a phase 4 DRAGEN server. For reference, phase 4 servers have a server serial number which begins with the letters "AC".
* MRJD requires at least 16x coverage to make calls; the caller will abort any attempt to call genes with insufficient aligned read coverage.

#### Variant Calling <a href="#variant-calling" id="variant-calling"></a>

* Any additional variant callers are not supported, and any data generated by them has not been validated
* Variant calling is only currently supported for human reference genomes
  * If required, non-human reference genomes must be uploaded in a v12 file format. These will not produce variant calls that the Illumina team supports.

### Downsampling

* Fractional downsampling is not supported in TruPath. This downsampling method disrupts proximity information, leading to degraded secondary analysis performance.


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